The interaction of electron acceptors with bases—II The spectrum of s-trinitrobenzene in the presence of ammonia and aliphatic amines

The interaction of s-trinitrobenzene with certain aliphatic amines has been studied spectrophotometrically. It is suggested in solutions in ethanol or chloroform, an adduct is initially formed by a dative bond between the nitrogen of the amine molecule and the 2-position in s-trinitrobenzene. The initial reactions are reversed by acid, but in time further irreversible reactions occur.     

Simple mean-field theory for a zero-temperature fermionic gas at a Feshbach resonance

We present a simple two-channel mean-field theory for a zero-temperature two-component Fermi gas in the neighborhood of a Feshbach resonance. Our results agree with recent experiments on the bare-molecule fraction as a function of magnetic field [Partridge, Phys. Rev. Lett. 95, 020404 (2005)]. Even in this strongly coupled gas of 6Li, the experimental results depend on the structure of the molecules formed in the Feshbach resonance and, therefore, are not universal.     

Pyrrolo-dC and pyrrolo-C: fluorescent analogs of cytidine and 2-deoxycytidine for the study of oligonucleotides

Pyrrolo-dC (1a, 6-methyl-3-(2-deoxy-β-d-ribofuranosyl)-3H-pyrrolo[2,3-d]pyrimidin-2-one) and its cyanoethyl phosphoramidite 2a were synthesized. The latter was incorporated into oligodeoxyribonucleotides by standard automated synthesis techniques, where pyrrolo-dC was found to serve as a fluorescent analog of deoxycytidine. The cyanoethylphosphoramidite (2b) of pyrrolo-C (2a, 6-methyl-3-(β-d-ribofuranosyl)-3H-pyrrolo[2,3-d]pyrimidin-2-one) was also synthesized and may find use for the site-specific incorporation of a fluorescent cytidine analog into oligoribonucleotides.     

Oxidation of CO by SO2: a theoretical study

The elementary reaction SO(2) + CO --> CO(2) + SO((3)Sigma) (1) and the subsequent reaction SO((3)Sigma) + CO --> CO(2) + S((3)P) (2) have been studied by the application of the Gaussian-3//B3LYP quantum chemical approach to characterize the potential energy surfaces and transition state kinetic analysis to derive rate coefficients. Reaction 1 is found to take place via two transition states (TS), a cis-OSOCO TS and a trans-OSOCO TS. Reaction via the cis-TS is concerted and takes place on a singlet surface. Intersystem crossing to the final products occurs after passage through the barrier on the singlet surface. The trans-TS leads to a very weakly bound singlet OSOCO intermediate that then passes through a second TS (on the triplet surface) to form the products. Reaction 2 takes place on triplet surfaces. There is a concerted reaction through a cis-SOCO TS and a weakly bound trans-SOCO has also been identified. Reaction 2 is analogous to the reaction CO + O(2)((3)Sigma) --> CO(2) + O((3)P) (3), and this reaction has been reinvestigated at a similar level of theory and the rate coefficient derived by quantum chemistry is compared with experiment. The sensitive effects of trace impurities such as H(2), H(2)O, and hydrocarbons on the accurate experimental determination of the rate coefficient of reaction 3 is discussed. Using rate coefficients for reactions 1 and 2 obtained via quantum chemical calculations, we have been unable to model the extent of decomposition of SO(2) measured in a shock tube study of reaction between SO(2) and CO [Bauer, S. H.; Jeffers, P.; Lifshitz, A.; Yadava, B. P. Proc. Combust. Inst. 1971, 13, 417]. In light of the known sensitivity of reaction 3 to trace impurities, we have incorporated trace amounts of H(2), CH(4), or H(2)O, together with our rate coefficients for (1) and (2), in a kinetic model of Alzueta et al. [Combust. Flame 2001, 127, 2234], which is then shown to be able to substantially model the SO(2) data of Bauer et al. In the course of this modeling study we also computed heats of formation for a number of sulfur-containing small molecules: HS, HSO, HSOH, HOSO, HS(2), HSO(2), HOSO(2), HOSOH, and HOSHO.     

Competitive adsorption of proteins and low-molecular-weight surfactants: computer simulation and microscopic imaging

Proteins and low-molecular-weight (LMW) surfactants are used in the food industry as emulsifying (and foaming) ingredients and as stabilizers. These attributes are related to their ability to adsorb at fluid-fluid (and gas-fluid) interfaces lowering the interfacial (and surface) tension of liquids. Hence, the study of the properties of adsorbed layers of these molecules can be expected to lead to a better understanding of their effect on food products. Direct proof of the validity of mesoscopic models of systems of proteins and LMW surfactants can only be achieved by quantitative theoretical predictions being tested against both macroscopic and mesoscopic experiments. Computer simulation constitutes one of the few available tools to predict mathematically the behaviour of models of realistic complexity. Furthermore, experimental techniques such as atomic force microscopy (AFM) now allow high resolution imaging of these systems, providing the mesoscopic scale measurements to compare with the simulations. In this review, we bring together a number of related findings that have been generated at this mesoscopic level over the past few years. A useful simple model consisting of spherical particles interacting via bonded and unbonded forces is described, and the derived computer simulation results are compared against those from the imaging experiments. Special attention is paid to the adsorption of binary mixtures of proteins, mixtures of LMW surfactants, and also protein+surfactant mixed systems. We believe that further development of these mathematically well-defined physical models is necessary in order to achieve a proper understanding of the key physico-chemical processes involved.     

Transport coefficients and dynamic properties of hydrogen sulfide from molecular simulation

Molecular-dynamics simulation results on thermodynamic and transport properties of pure H2S under conditions of practical interest are presented. Our data are in very good quantitative agreement with the scarce experimental data and estimates on thermophysical properties of this substance. Our results serve as a test of the validity of the intermolecular potential used in the simulations as well as the consistency of the existing data in the studied range. New simulation data on thermal conductivity at low temperature as well as in supercritical states are also reported. Furthermore, we present a comparative analysis between the local order in the liquid phase of pure hydrogen sulfide and water, due to the molecular analogies between both substances, and its relation with the formation of H=S bonds. Our results indicate that under the same corresponding thermodynamic states, H2S is a much less structured substance, with a first solvation shell with a dodecahedral order instead of the tetrahedral order observed in water.     

Atomic force microscopy of emulsion droplets: probing droplet-droplet interactions

A method has been developed for attaching oil (tetradecane) droplets to the end of an atomic force microscopy (AFM) cantilever and for immobilizing droplets on a glass substrate. This approach has permitted the monitoring of droplet-droplet interactions in aqueous solution as a function of interdroplet separation. Coating the droplet surfaces with added proteins or surfactants has allowed the production of model emulsions. We demonstrate that AFM measurements of droplet deformability are sensitive to interfacial rheology by modifying the interfacial film on a pair of droplets in situ. For droplets coated with the anionic surfactant sodium dodecyl sulfate, screening of the double layer has been found to facilitate coalescence. Direct imaging of the droplets has revealed the presence of regularly spaced concentric rings on the droplet surfaces. Careful experimental studies suggest that these structures may be imaging artifacts and are not perturbations of the droplet surface determined by the composition of the interface.     

Optimizing separations in reversed-phase liquid chromatography by varying pH and solvent composition

Summary An interpretive optimization procedure in which pH can be one of the variables is presented with the emphasis on optimizing separations. When varying the pH in reversed-phase liquid chromatography the retention of ionogenic solutes will change. Thus, the selectivity between ionogenic and neutral solutes or between ionogenic solutes mutually can be optimized. However, pH also greatly affects the efficiency (plate count) and peak shape (asymmetry). Optimum selectivity (i.e. large differences in retention times) may be observed under conditions where peaks are broad and asymmetrical. Thus, it is essential to simultaneously consider retention, peak width and peak shape and their effects on separation (effective resolution) in pH-optimization studies. A procedure in which this is done is presented and applied to optimizing the separation of a synthetic mixture of selected pharmaceuticals. After initial experiments to establish the parameter space (boundaries for pH and binary methanol — water composition), twelve experiments are performed according to a 3×4 experimental design. At each loaction the retention, peak height, peak area and peak symmetry are recorded for each solute. These data are then used to build models for each of the four characteristics and for each solute. From this set of models the response surface, describing the quality of separation as a function of pH and composition, can be calculated. A variety of optimization criteria (quantifying quality of separation) can be used. The optimum corresponds to the highest point on the response surface.     

Thermochemical and kinetic study of the carbocation ring contraction of cyclohexylium to methylcyclopentylium

The isomerization of cyclohexylium to methylcyclopentylium is a model for a key step required in sterol and triterpene biosynthesis and is important in catalytic processes associated with ring-opening reactions in upgrading petroleum fractions. Using high-level, correlated wave function techniques based on QCISD, the mechanism for this isomerization was found to be very different from that first proposed more than 35 years ago. On the basis of our mechanism, a first-order rate constant expression was derived and used with complete basis set-extrapolated QCISD(T) energies to obtain Ea = 6.9 kcal/mol and A = 1011.18 s-1, in excellent agreement with values of 7.4 +/- 1 kcal/mol and A = 1012 +/- 1.3 s-1 measured in the gas phase. The B3LYP and MP2 methods, two commonly used computational approaches, were found to predict incorrect mechanisms and, in some cases, poor kinetic parameters. The PBE method, however, produced a reaction profile and kinetic parameters in reasonable agreement with those obtained with the complete basis set-extrapolated QCISD(T) method.     

Reaction of phenols with the 2,2-diphenyl-1-picrylhydrazyl radical. Kinetics and DFT calculations applied to determine ArO-H bond dissociation enthalpies and reaction mechanism

The formal H-atom abstraction by the 2,2-diphenyl-1-picrylhydrazyl (dpph(*)) radical from 27 phenols and two unsaturated hydrocarbons has been investigated by a combination of kinetic measurements in apolar solvents and density functional theory (DFT). The computed minimum energy structure of dpph(*) shows that the access to its divalent N is strongly hindered by an ortho H atom on each of the phenyl rings and by the o-NO(2) groups of the picryl ring. Remarkably small Arrhenius pre-exponential factors for the phenols [range (1.3-19) x 10(5) M(-1) s(-1)] are attributed to steric effects. Indeed, the entropy barrier accounts for up to ca. 70% of the free-energy barrier to reaction. Nevertheless, rate differences for different phenols are largely due to differences in the activation energy, E(a,1) (range 2 to 10 kcal/mol). In phenols, electronic effects of the substituents and intramolecular H-bonds have a large influence on the activation energies and on the ArO-H BDEs. There is a linear Evans-Polanyi relationship between E(a,1) and the ArO-H BDEs: E(a,1)/kcal x mol(-1) = 0.918 BDE(ArO-H)/kcal x mol(-1) - 70.273. The proportionality constant, 0.918, is large and implies a "late" or "product-like" transition state (TS), a conclusion that is congruent with the small deuterium kinetic isotope effects (range 1.3-3.3). This Evans-Polanyi relationship, though questionable on theoretical grounds, has profitably been used to estimate several ArO-H BDEs. Experimental ArO-H BDEs are generally in good agreement with the DFT calculations. Significant deviations between experimental and DFT calculated ArO-H BDEs were found, however, when an intramolecular H-bond to the O(*) center was present in the phenoxyl radical, e.g., in ortho semiquinone radicals. In these cases, the coupled cluster with single and double excitations correlated wave function technique with complete basis set extrapolation gave excellent results. The TSs for the reactions of dpph(*) with phenol, 3- and 4-methoxyphenol, and 1,4-cyclohexadiene were also computed. Surprisingly, these TS structures for the phenols show that the reactions cannot be described as occurring exclusively by either a HAT or a PCET mechanism, while with 1,4-cyclohexadiene the PCET character in the reaction coordinate is much better defined and shows a strong pi-pi stacking interaction between the incipient cyclohexadienyl radical and a phenyl ring of the dpph(*) radical.